Electron energy loss spectroscopic imaging has been implemented in a transmission electron microscope equipped with a post-column energy filter to extract quantitative elemental maps from biological specimens. Series of up to one hundred 1024x1024 pixel energy-selected images have been recorded by means of a cooled CCD camera coupled to a single crystal YAG scintillator which provides a detective quantum efficiency close to unity. Individual images in each series are first cross-correlated to correct for specimen drift. Spectra are then extracted for each pixel and the net core-edge intensity obtained by extrapolating the background and integrating the signal in a specified energy range. The advantage of spectrum-imaging over the conventional two-window or three-window EELS mapping techniques is the increased accuracy that is attainable. Furthermore, spectrum-imaging in the energy-filtering transmission electron microscope (EFTEM) can be used to acquire elemental maps from larger sample areas than would be achievable in the scanning transmission electron microscope (STEM), although the minimum detectable concentrations are lower in the STEM. Spectrum-imaging in the EFTEM has been applied to map intracellular phosphorus, sulfur and calcium.